Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 70.47 kDa 
• Atom Count: 4928 
• Modelled Residue Count: 604 
• Deposited Residue Count: 616 
• Unique protein chains: 2

6SC6

dAb3/HOIP-RBR apo structure

• PDB DOI: 10.2210/pdb6SC6/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-23 Released: 2019-11-27 
• Deposition Author(s): Tsai, Y.-C.I., House, D., Rittinger, K.
• Funding Organization(s): The Francis Crick Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases.

Tsai, Y.I., Johansson, H., Dixon, D., Martin, S., Chung, C.W., Clarkson, J., House, D., Rittinger, K.

(2020) Cell Chem Biol 27: 83

• PubMed: 31813847 
• DOI: 10.1016/j.chembiol.2019.11.007
• Primary Citation of Related Structures:  
  6SC5, 6SC6, 6SC7, 6SC8, 6SC9, 6T2J


• PubMed Abstract: 
  

Protein ubiquitination plays a key role in the regulation of cellular processes, and misregulation of the ubiquitin system is linked to many diseases. So far, development of tool compounds that target enzymes of the ubiquitin system has been slow and only a few specific inhibitors are available. Here, we report the selection of single-domain antibodies (single-dAbs) based on a human scaffold that recognize the catalytic domain of HOIP, a subunit of the multi-component E3 LUBAC and member of the RBR family of E3 ligases. Some of these dAbs affect ligase activity and provide mechanistic insight into the ubiquitin transfer mechanism of different E2-conjugating enzymes. Furthermore, we show that the co-crystal structure of a HOIP RBR/dAb complex serves as a robust platform for soaking of ligands that target the active site cysteine of HOIP, thereby providing easy access to structure-based ligand design for this important class of E3 ligases.

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Organizational Affiliation: 

Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF31	A	376	Homo sapiens	Mutation(s): 0  Gene Names: RNF31, ZIBRA EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EP0 (Homo sapiens) Explore Q96EP0  Go to UniProtKB:  Q96EP0
PHAROS:  Q96EP0 GTEx:  ENSG00000092098

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Single domain antibody	B, C	120	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	O [auth A], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.948	α = 90
b = 87.49	β = 90
c = 241.927	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-07-23 
• Released Date: 2019-11-27 
Deposition Author(s): Tsai, Y.-C.I., House, D., Rittinger, K.

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Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	--

Revision History  

• Version 1.0: 2019-11-27
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references
• Version 1.2: 2020-01-29
  Changes: Database references